Contacts of the helix formed by residues 493 - 508 (chain A) in PDB entry 3OAA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A TYR* 1.3 86.3 - - - +
494A ASP* 1.3 74.9 + - - +
495A GLU* 2.7 35.0 + - - +
496A ILE* 3.0 25.4 + - + +
497A GLU* 2.9 22.2 + - - +
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Residues in contact with ASP 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A TYR* 4.7 4.8 - - - -
493A ASN* 1.3 80.5 - - - +
495A GLU* 1.3 62.8 + - - +
497A GLU* 3.3 22.2 - - - +
498A GLY* 3.5 3.8 + - - -
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A GLU* 5.3 0.9 - - - +
493A ASN* 2.7 18.3 + - - +
494A ASP* 1.3 72.4 - - - +
496A ILE* 1.3 86.1 + - - +
498A GLY* 3.0 14.4 + - - -
499A LYS* 3.1 38.9 + - + +
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Residues in contact with ILE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A ILE* 5.1 0.2 - - + -
485A GLU* 4.4 18.8 - - - +
486A ILE* 3.9 28.9 - - + -
491A GLY 4.9 3.1 - - - +
492A TYR* 4.5 8.3 - - + -
493A ASN* 3.0 40.4 + - + +
495A GLU* 1.3 95.9 - - - +
497A GLU* 1.3 62.0 + - - +
499A LYS* 3.4 14.1 + - + +
500A LEU* 3.1 34.8 + - + +
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Residues in contact with GLU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A PHE* 3.2 25.1 - - - -
452A GLU* 2.9 28.2 - - - +
492A TYR* 3.2 35.5 + - - +
493A ASN 2.9 7.7 + - - +
494A ASP* 3.3 16.8 - - - +
495A GLU 3.1 0.2 - - - -
496A ILE* 1.3 76.7 - - - +
498A GLY* 1.3 60.3 + - - +
500A LEU* 3.3 9.6 + - - +
501A LYS* 3.0 41.4 + - - +
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Residues in contact with GLY 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A ASP 3.5 3.9 + - - -
495A GLU 3.0 7.2 + - - -
497A GLU* 1.3 80.4 - - - +
499A LYS* 1.3 66.3 + - - +
501A LYS* 3.0 21.9 + - - +
502A GLY* 3.1 11.4 + - - -
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Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A LEU* 3.6 42.7 + - + +
485A GLU* 4.2 16.2 + - - -
495A GLU* 3.1 43.7 + - + +
496A ILE* 3.6 15.0 - - + +
498A GLY* 1.3 77.0 - - - +
500A LEU* 1.3 63.1 + - + +
502A GLY* 3.5 2.3 + - - -
503A ILE* 3.0 26.3 + - + +
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A ILE* 4.7 5.8 - - + -
389A LEU* 6.5 0.9 - - + -
444A GLN* 4.2 24.7 - - + +
445A SER* 4.4 21.5 - - - +
448A LEU* 5.8 3.4 - - + -
449A PHE* 3.2 35.8 - - + -
476A ASP* 5.8 1.8 - - - +
486A ILE* 5.6 1.1 - - + -
492A TYR* 5.1 4.9 - - + -
496A ILE* 3.1 32.5 + - + +
497A GLU* 3.4 6.5 - - - +
499A LYS* 1.3 74.5 - - + +
501A LYS* 1.3 66.2 + - - +
503A ILE* 2.9 37.3 + - + +
504A LEU* 3.4 5.2 + - - +
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Residues in contact with LYS 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A PHE* 3.1 15.6 - - + -
452A GLU* 5.8 6.3 - - - -
453A ARG* 6.5 1.8 - - - -
455A TYR* 3.5 19.1 + - - +
497A GLU* 3.0 34.8 + - - +
498A GLY* 3.0 14.1 + - - +
500A LEU* 1.3 75.4 - - - +
502A GLY* 1.3 62.2 + - - +
504A LEU* 3.3 2.6 + - - -
505A ASP* 3.1 37.4 + - - +
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Residues in contact with GLY 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A GLY 3.1 11.5 + - - -
499A LYS 3.5 3.8 + - - -
500A LEU 3.2 0.2 - - - -
501A LYS* 1.3 77.7 - - - +
503A ILE* 1.3 57.3 + - - +
505A ASP* 3.8 9.0 - - - +
506A SER* 2.8 33.0 + - - -
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A LEU* 5.2 2.7 - - + -
475A VAL* 4.9 9.2 - - + +
476A ASP* 4.5 23.1 - - + +
479A HIS* 3.4 41.3 - - + +
482A LEU* 5.5 10.3 - - + +
483A MET* 6.2 1.6 - - + +
499A LYS* 3.0 22.4 - - + +
500A LEU* 2.9 31.6 + - + +
502A GLY* 1.3 77.6 - - - +
504A LEU* 1.3 61.8 + - + +
506A SER* 3.8 6.1 - - - -
507A PHE* 3.1 23.4 + - - +
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Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A SER* 5.4 4.0 - - - +
449A PHE* 3.2 43.1 - - + +
450A ALA* 5.4 0.2 - - - -
455A TYR* 3.3 46.7 - - + -
468A GLU* 5.5 0.7 - - - +
472A LEU* 3.4 45.5 - - + -
500A LEU 3.4 2.6 + - - +
501A LYS 3.3 4.3 + - - +
502A GLY 3.2 0.4 - - - -
503A ILE* 1.3 82.0 - - + +
505A ASP* 1.3 65.7 + - - +
506A SER 3.2 1.3 - - - -
507A PHE* 3.0 18.9 + - + +
508A LYS* 3.0 19.8 + - + +
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Residues in contact with ASP 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A TYR* 2.9 29.6 + - - -
501A LYS* 3.1 31.2 + - - +
502A GLY* 3.8 7.5 - - - +
504A LEU* 1.3 75.0 - - - +
506A SER* 1.3 61.4 + - - +
508A LYS* 3.2 22.9 + - - +
509A ALA* 5.2 1.0 - - - +
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Residues in contact with SER 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A GLY 2.8 18.8 + - - -
503A ILE* 3.8 7.4 - - - -
505A ASP* 1.3 77.2 - - - +
507A PHE* 1.3 61.1 + - - +
508A LYS 3.3 0.5 + - - -
509A ALA* 3.5 17.1 + - - +
510A THR* 4.0 6.9 + - - -
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Residues in contact with PHE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A GLU* 3.2 36.8 - - - -
471A LEU* 3.8 15.9 - - + -
472A LEU* 3.4 41.1 - - + -
475A VAL* 3.4 31.2 - - + -
503A ILE 3.1 16.4 + - - +
504A LEU* 3.0 20.7 + - + +
506A SER* 1.3 72.0 - - - +
508A LYS* 1.3 63.4 + - + +
509A ALA 2.8 17.5 + - - -
510A THR* 3.1 39.6 + - + +
511A GLN* 5.4 6.7 - - + -
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Residues in contact with LYS 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A TYR* 2.8 47.0 + - + +
458A ASP* 3.0 24.9 + - - +
459A VAL* 4.7 9.0 - - - +
468A GLU* 4.7 6.5 - - - -
504A LEU* 3.0 16.3 + - + +
505A ASP* 3.4 17.2 - - - +
506A SER 3.1 0.8 - - - -
507A PHE* 1.3 88.7 - - + +
509A ALA* 1.3 59.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il